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Toxicol Sci. 2018 Mar 1;162(1):264-275. doi: 10.1093/toxsci/kfx252.

A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions.

Author information

1
Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden.
2
Department of Toxicology, Misvik Biology, 20520 Turku, Finland.
3
Department of Bioinformatics, NUTRIM, Maastricht University, 6200MD Maastricht, The Netherlands.
4
Division of Environmental Health Sciences, School of Public Health, University of California, 94720-7360 Berkeley, California, United States.
5
IdeaConsult Ltd, 1000 Sofia, Bulgaria.
6
School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece.
7
Institute for the Management of Information Systems, ATHENA Research and Innovation Centre, 151 25 Athens, Greece.

Abstract

Increasing amounts of systems toxicology data, including omics results, are becoming publically available and accessible in databases. Data-driven and informatics-tool supported pipeline schemas for fitting such data into Adverse Outcome Pathway (AOP) descriptions could potentially aid the development of nonanimal-based hazard and risk assessment methods. We devised a 6-step workflow that integrated diverse types of toxicology data into a novel AOP scheme for pulmonary fibrosis. Mining of literature references and diverse data sources covering previous pathway descriptions and molecular results were coupled in a stepwise manner with informatics tools applications that enabled gene linkage and pathway identification in molecular interaction maps. Ultimately, a network of functional elements coupled 64 pulmonary fibrosis-associated genes into a novel, open-source AOP-linked molecular pathway, now available for commenting and improvements in WikiPathways (WP3624). Applying in silico-based knowledge extraction and modeling, the pipeline enabled screening and fusion of many different complex data types, including the integration of omics results. Overall, the taken, stepwise approach should be generally useful to construct novel AOP descriptions as well as to enrich developing AOP descriptions in progress.

PMID:
29149350
DOI:
10.1093/toxsci/kfx252
[Indexed for MEDLINE]

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